rs1360180

Variant names:

• chr1-68246675-G-A
• rs1360180

Your query was ambiguous. Multiple possible variants found:

• chr1-68246675-G-A
• chr1-68246675-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.108 in 152,032 control chromosomes in the GnomAD database, including 1,025 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16444 AN: 151914 Hom.: 1022 Cov.: 32

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.130

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.108 AC: 16436 AN: 152032 Hom.: 1025 Cov.: 32 AF XY: 0.108 AC XY: 8062 AN XY: 74310

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0873

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0714

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.128

Alfa AF: 0.122 Hom.: 1615

Bravo AF: 0.114

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1360180; hg19: chr1-68712358;